Cyndaquil seems to be quite underwhelming at first glance, due to its poor movepool and average stats. There is some truth to this, as Houndour is a better special attacker, while Ponyta is a much better physical attacker. However, Cyndaquil has one saving grace as the only Pokemon in Little Cup to learn Eruption. When at full health, it can hit many things that don't resist Fire-type attacks quite hard. Despite needing some team support in the form of Rapid Spin, Cyndaquil can be a good choice in Little Cup provided it maintains its niche.
Reaching 16 Special Attack and 24 Speed with a Choice Scarf, Cyndaquil can be used as a powerful attacker and revenge killer when healthy. Eruption is extremely powerful at high health. When Cyndaquil falls below 80% of its maximum HP, however, Fire Blast becomes the more powerful option. Hidden Power Grass is Cyndaquil's main coverage move, hitting Water-types which resist Eruption hard. Nature Power becomes Earthquake in a Wi-Fi environment, including on simulators, meaning it is the best option to hit Houndour, Tentacool, and Ponyta.Team Options & Additional Comments >>>
Cyndaquil has few good options, and the main set is easily its best. Extrasensory can hit Tentacool for super effective damage, but Cyndaquil already has Nature Power to deal with it. Flame Charge can be used to boost Speed without resorting to a Choice Scarf. Both sacrifice coverage options in Nature Power or Hidden Power or reliability in Fire Blast, meaning they are lesser options.
Cyndaquil also has a decent physical movepool, with Flame Charge, Nature Power, Flare Blitz, and Wild Charge. Sadly, it packs too little power, and Ponyta completely outclasses it outside of Nature Power.
Checks and Counters
Houndour and Ponyta are the best counters to this set. They can switch in with ease thanks to Flash Fire and resistance to Grass-type attacks, and smack Cyndaquil with Dark Pulse or Return, respectively. However, they need to watch out for Nature Power.
Water-types work well, as they resist Fire-type attacks. Slowpoke, Chinchou, and Frillish can work nicely with their good bulk, but need to watch out for Hidden Power Grass. Tentacool can handle Hidden Power but can't take Nature Power. It has high Special Defense, making it a good choice with a little prediction.
Revenge killing is another option to beat Cyndaquil. Mienfoo with Eviolite can survive Eruption and KO back. Mienfoo gets the KO with Fake Out followed by Drain Punch.
Cyndaquil gets Flash Fire as a Dream World ability, and at first glance it seems to be the obvious option. Sadly, it has not been released. All starter Pokemon with Dream World abilities released so far have been level 10 and male, meaning it would likely be illegal in Little Cup if it were released.